rs10890920

Variant names:

• chr11-109002392-G-A
• rs10890920
• ENST00000526041.2:n.464C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-109002392-G-A
• chr11-109002392-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000526041.2(ENSG00000255528):​n.464C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,118 control chromosomes in the GnomAD database, including 19,571 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.49 (19567 hom., cov: 33)
  • Exomes 𝑓: 0.65 (4 hom.)
• Consequence: ENSG00000255528 ENST00000526041.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 5 publications found

Genes affected

ENSG00000255528 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255528	ENST00000526041.2	n.464C>T		non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73996 AN: 151980 Hom.: 19558 Cov.: 33

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.508

GnomAD4 exome AF: 0.650 AC: 13 AN: 20 Hom.: 4 AF XY: 0.611 AC XY: 11 AN XY: 18

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 2 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 4 AN: 4

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.500 AC: 5 AN: 10

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.487 AC: 74023 AN: 152098 Hom.: 19567 Cov.: 33 AF XY: 0.490 AC XY: 36445 AN XY: 74338

African (AFR) AF: 0.273 AC: 11320 AN: 41480

American (AMR) AF: 0.555 AC: 8491 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2237 AN: 3468

East Asian (EAS) AF: 0.641 AC: 3308 AN: 5164

South Asian (SAS) AF: 0.555 AC: 2675 AN: 4822

European-Finnish (FIN) AF: 0.555 AC: 5853 AN: 10554

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38318 AN: 67992

Other (OTH) AF: 0.510 AC: 1080 AN: 2116

Alfa AF: 0.543 Hom.: 101734

Bravo AF: 0.474

Asia WGS AF: 0.615 AC: 2137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.77
DANN	Benign	0.60
PhyloP100		0.16
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10890920; hg19: chr11-108873119;